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- PDB-7p18: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Ster... -

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Basic information

Entry
Database: PDB / ID: 7p18
TitleCrystal structure of 3-ketosteroid delta1-dehydrogenase from Sterolibacterium denitrificans in complex with 1,4-androstadiene-3,17-dione
Components3-oxosteroid 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Flavoprotein / Dehydrogenase / 3-Ketosteroid Delta1-dehydrogenase / 3-Ketosteroid Dehydrogenase / 3-Oxosteroid Dehydrogenase / Rossmann Fold
Function / homology
Function and homology information


3-oxosteroid 1-dehydrogenase / 3-oxosteroid 1-dehydrogenase activity / steroid metabolic process / nucleotide binding
Similarity search - Function
: / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ANDROSTA-1,4-DIENE-3,17-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / 3-oxosteroid 1-dehydrogenase
Similarity search - Component
Biological speciesSterolibacterium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsWojcik, P. / Mrugala, B. / Kurpiewska, K. / Szaleniec, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2016/21/B/ST4/03798 Poland
Citation
Journal: Biochemistry / Year: 2023
Title: Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans ─The Role of a New Putative Membrane-Associated Domain and Proton- ...Title: Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans ─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis.
Authors: Wojcik, P. / Glanowski, M. / Mrugala, B. / Procner, M. / Zastawny, O. / Flejszar, M. / Kurpiewska, K. / Niedzialkowska, E. / Minor, W. / Oszajca, M. / Bojarski, A.J. / Wojtkiewicz, A.M. / Szaleniec, M.
#1: Journal: Int J Mol Sci / Year: 2022
Title: 1,2-Hydrogenation and Transhydrogenation Catalyzed by 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans -Kinetics, Isotope Labelling and QM:MM Modelling Studies.
Authors: Wojtkiewicz, A.M. / Glanowski, M. / Waligorski, P. / Janeczko, T. / Szaleniec, M.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Revision 1.3Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxosteroid 1-dehydrogenase
B: 3-oxosteroid 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,54114
Polymers122,8562
Non-polymers2,68512
Water14,880826
1
A: 3-oxosteroid 1-dehydrogenase
hetero molecules


  • defined by author&software
  • Evidence: microscopy, K. Sofinska, A. M. Wojtkiewicz, P. Wojcik, O. Zastawny, M. Guzika, A. Winiarska, P. Waligorski, M. Ciesla, J. Barbasz, M. Szaleniec, Investigation of quaternary structure of ...Evidence: microscopy, K. Sofinska, A. M. Wojtkiewicz, P. Wojcik, O. Zastawny, M. Guzika, A. Winiarska, P. Waligorski, M. Ciesla, J. Barbasz, M. Szaleniec, Investigation of quaternary structure of aggregating 3-ketosteroid dehydrogenase from Sterolibacterium denitrificans: In the pursuit of consensus of various biophysical techniques, BBA - General Subjects, 1863 (2019) 1027-1039, gel filtration, The monomeric fraction of the protein was obtained in 50 mM Tris-HCl pH 8.5, 150 mM NaCl, 0.2% Tween 20, 0.5 mM TCEP.
  • 63.1 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)63,11510
Polymers61,4281
Non-polymers1,6889
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-oxosteroid 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4264
Polymers61,4281
Non-polymers9983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.369, 130.369, 139.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 5 - 560 / Label seq-ID: 5 - 560

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-oxosteroid 1-dehydrogenase / Cholest-4-en-3-one-delta1-dehydrogenase


Mass: 61427.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sterolibacterium denitrificans (bacteria)
Gene: acmB, SDENCHOL_10486 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Magic / References: UniProt: A9XWD7, 3-oxosteroid 1-dehydrogenase

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Non-polymers , 6 types, 838 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ANB / ANDROSTA-1,4-DIENE-3,17-DIONE


Mass: 284.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 826 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.48 % / Description: bright yellow rhombohedral crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 293 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2021
RadiationMonochromator: DCM Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.84→47.71 Å / Num. obs: 119085 / % possible obs: 99.52 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.057 / Rrim(I) all: 0.07 / Rsym value: 0.129 / Net I/av σ(I): 1.6 / Net I/σ(I): 1.6
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.719 / Num. unique obs: 5860 / CC1/2: 0.515 / Rpim(I) all: 0.753 / Rrim(I) all: 0.486 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrysalisProdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3Y

4c3y


Resolution: 1.84→47.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.25 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21401 2100 1.8 %RANDOM
Rwork0.18461 ---
obs0.18514 116410 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.846 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å2-0 Å2
3----1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.84→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8567 0 181 826 9574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178317
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.64512321
X-RAY DIFFRACTIONr_angle_other_deg1.3671.57619282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03151135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02721.688462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34151445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6951565
X-RAY DIFFRACTIONr_chiral_restr0.0760.21121
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021939
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.173.5894513
X-RAY DIFFRACTIONr_mcbond_other3.1683.5894512
X-RAY DIFFRACTIONr_mcangle_it4.2425.3765657
X-RAY DIFFRACTIONr_mcangle_other4.2425.3775658
X-RAY DIFFRACTIONr_scbond_it3.6693.9744561
X-RAY DIFFRACTIONr_scbond_other3.6683.9744562
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3735.8146665
X-RAY DIFFRACTIONr_long_range_B_refined7.37742.79710493
X-RAY DIFFRACTIONr_long_range_B_other7.28942.4710288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18580 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.84→1.887 Å
RfactorNum. reflection% reflection
Rfree0.299 152 -
Rwork0.278 8438 -
obs--98.69 %

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